Contacts of the strand formed by residues 208 - 215 (chain H) in PDB entry 2BDI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 208 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H ILE* 4.3 1.1 - - - -
122H SER* 3.6 23.8 - - - -
123H ILE 4.3 3.6 - - - -
124H ALA* 3.7 33.2 - - + -
125H SER 5.5 2.2 - - - -
200H ILE* 2.9 8.6 - - - +
201H CYS 2.7 34.7 + - - +
202H ASN* 2.9 28.3 - - + -
203H GLY* 1.3 83.8 - - - +
209H LEU* 1.3 60.6 + - - +
210H GLN* 3.2 2.0 + - - +
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Residues in contact with LEU 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H VAL* 3.6 30.5 - - + -
47H VAL* 3.8 9.4 - - + -
53H LEU* 4.1 4.3 - - + -
121H ILE* 4.1 9.0 - - + +
122H SER 2.8 19.3 + - - +
123H ILE* 3.5 28.1 - - + +
124H ALA* 2.7 27.6 + - - +
198H PRO* 3.9 13.7 - - + -
199H LEU 4.2 0.2 - - - +
200H ILE* 3.9 20.4 - - + -
208H TYR* 1.3 68.5 - - - +
210H GLN* 1.3 57.8 + - - +
211H GLY 3.7 19.7 - - - +
212H LEU* 5.4 0.4 - - + -
231H LEU* 3.6 17.6 - - + +
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Residues in contact with GLN 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ALA* 3.8 16.1 - - - +
127H GLN 3.0 24.8 + - - +
128H CYS 3.8 0.6 - - - -
129H PRO* 3.3 37.9 - - + +
181H PHE* 3.9 11.6 - - + -
199H LEU* 2.7 17.0 + - + +
201H CYS* 3.4 45.6 + - + +
208H TYR* 3.2 1.8 + - - +
209H LEU* 1.3 73.7 - - - +
211H GLY* 1.3 56.5 + - - +
229H THR 3.8 1.0 - - - +
230H ASN* 4.7 1.0 - - - +
231H LEU* 3.4 24.7 + - - +
232H CYS* 4.5 4.5 + - - +
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Residues in contact with GLY 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H PHE* 4.0 9.2 - - - -
197H GLY 3.5 1.9 - - - +
198H PRO* 3.5 3.3 - - - +
199H LEU* 2.9 39.2 + - - +
209H LEU* 3.7 6.1 - - - +
210H GLN* 1.3 80.7 - - - +
212H LEU* 1.3 66.0 + - - +
228H TYR* 4.5 0.7 - - - -
229H THR 3.3 12.6 - - - -
231H LEU* 3.5 7.0 - - - +
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Residues in contact with LEU 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H VAL* 4.2 15.5 - - + -
53H LEU* 4.0 12.1 - - + +
54H SER* 3.4 33.4 - - - +
55H ALA* 4.4 1.6 - - + +
102H ASP 4.5 0.7 - - - +
103H LEU* 4.1 9.4 - - + -
196H GLY* 3.0 33.0 - - - +
197H GLY 2.9 6.5 - - - +
209H LEU* 5.3 0.2 - - + -
211H GLY* 1.3 79.7 - - - +
213H VAL* 1.3 66.4 + - - +
228H TYR* 3.0 9.8 - - - -
229H THR* 2.9 40.0 + - - +
231H LEU* 3.8 27.6 - - + -
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Residues in contact with VAL 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H ALA* 4.2 3.5 - - - +
138H VAL* 4.3 16.2 - - + -
139H SER 5.3 0.7 - - - +
190H SER* 4.1 7.9 - - - +
194H ASP* 2.9 46.0 - - + +
195H SER* 3.2 7.5 - - - +
196H GLY* 2.6 27.4 + - - -
197H GLY* 2.8 24.8 + - - +
198H PRO 4.8 0.2 - - - +
212H LEU* 1.3 70.1 - - - +
214H SER* 1.4 57.5 + - - +
227H VAL 5.3 0.2 - - - +
228H TYR* 3.6 23.3 - - + -
708H PBZ 4.0 21.3 - - + -
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Residues in contact with SER 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G GLN* 3.3 3.8 - - - -
55H ALA* 5.3 0.2 - - - -
57H HIS* 3.0 23.1 - - - -
99H LEU 4.5 1.4 + - - -
102H ASP* 2.8 31.2 + - - +
180H MET* 6.2 0.4 - - - -
212H LEU 3.0 4.6 + - - -
213H VAL* 1.4 71.5 - - - +
215H PHE* 1.3 82.3 + - - +
227H VAL* 3.2 18.3 + - - -
228H TYR 4.3 0.9 - - - -
229H THR* 4.0 17.9 - - - -
708H PBZ 3.6 9.3 - - - -
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Residues in contact with PHE 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G GLN* 3.5 16.6 - + + +
222G VAL* 4.4 8.1 - - + -
99H LEU* 4.0 41.5 - - + -
172H TYR* 3.8 19.7 - + + -
175H LEU* 5.2 8.5 - - + -
180H MET* 3.7 23.6 - - + -
214H SER* 1.3 95.8 - - - +
216H GLY* 1.3 61.0 + - - +
227H VAL* 2.7 70.1 + - + +
708H PBZ 3.4 19.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il